public class PeptideVariantsPreferences extends Object implements Serializable
Constructor and Description |
---|
PeptideVariantsPreferences()
Constructor.
|
Modifier and Type | Method and Description |
---|---|
AaSubstitutionMatrix |
getAaSubstitutionMatrix()
Returns the amino acid substitution matrix to use.
|
Integer |
getnAaDeletions()
Returns the number of amino acid deletions allowed.
|
Integer |
getnAaInsertions()
Returns the number of amino acid insertions allowed.
|
Integer |
getnAaSubstitutions()
Returns the number of amino acid substitutions allowed.
|
Integer |
getnAaSwap()
Returns the number of amino acid swaps allowed.
|
static PeptideVariantsPreferences |
getNoVariantPreferences()
Returns the preferences corresponding to no variants allowed.
|
Integer |
getnVariants()
Returns the total number of variants allowed.
|
String |
getShortDescription()
Returns a short description of the parameters.
|
Boolean |
getUseSpecificCount()
Returns whether the specific variant count limitations should be used.
|
boolean |
isSameAs(PeptideVariantsPreferences peptideVariantsPreferences)
Indicates whether another peptide variant preferences is the same as this
one.
|
void |
setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)
Sets the amino acid substitution matrix to use.
|
void |
setnAaDeletions(Integer nAaDeletions)
Sets the number of amino acid deletions allowed.
|
void |
setnAaInsertions(Integer nAaInsertions)
Sets the number of amino acid insertions allowed.
|
void |
setnAaSubstitutions(Integer nAaSubstitutions)
Sets the number of amino acid substitutions allowed.
|
void |
setnAaSwap(Integer nAaSwap)
Sets the number of amino acid swaps allowed.
|
void |
setnVariants(Integer nVariants)
Sets the total number of variants allowed.
|
void |
setUseSpecificCount(Boolean useSpecificCount)
Sets whether the specific variant count limitations should be used.
|
public Integer getnAaDeletions()
public void setnAaDeletions(Integer nAaDeletions)
nAaDeletions
- the number of amino acid deletions allowedpublic Integer getnAaInsertions()
public void setnAaInsertions(Integer nAaInsertions)
nAaInsertions
- the number of amino acid insertions allowedpublic Integer getnAaSubstitutions()
public void setnAaSubstitutions(Integer nAaSubstitutions)
nAaSubstitutions
- the number of amino acid substitutions allowedpublic Integer getnAaSwap()
public void setnAaSwap(Integer nAaSwap)
nAaSwap
- the number of amino acid swaps allowedpublic AaSubstitutionMatrix getAaSubstitutionMatrix()
public void setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)
aaSubstitutionMatrix
- the amino acid substitution matrix to usepublic Boolean getUseSpecificCount()
public void setUseSpecificCount(Boolean useSpecificCount)
useSpecificCount
- a boolean indicating whether the specific variant
count limitations should be usedpublic Integer getnVariants()
public void setnVariants(Integer nVariants)
nVariants
- the total number of variants allowedpublic boolean isSameAs(PeptideVariantsPreferences peptideVariantsPreferences)
peptideVariantsPreferences
- the other preferencespublic String getShortDescription()
public static PeptideVariantsPreferences getNoVariantPreferences()
Copyright © 2018. All rights reserved.